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Si HR, Wu K, Su J, Dong TY, Zhu Y, Li B, Chen Y, Li Y, Shi ZL, Zhou P. Individual virome analysis reveals the general co-infection of mammal-associated viruses with SARS-related coronaviruses in bats. Virol Sin 2024; 39:565-573. [PMID: 38945213 DOI: 10.1016/j.virs.2024.06.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Accepted: 06/19/2024] [Indexed: 07/02/2024] Open
Abstract
Bats are the natural reservoir hosts for SARS-related coronavirus (SARSr-CoV) and other highly pathogenic microorganisms. Therefore, it is conceivable that an individual bat may harbor multiple microbes. However, there is limited knowledge on the overall co-circulation of microorganisms in bats. Here, we conducted a 16-year monitoring of bat viruses in south and central China and identified 238 SARSr-CoV positive samples across nine bat species from ten provinces or administrative districts. Among these, 76 individual samples were selected for further metagenomics analysis. We found a complex microenvironment characterized by the general co-circulation of microbes from two different sources: mammal-associated viruses or environment-associated microbes. The later includes commensal bacteria, enterobacteria-related phages, and insect or fungal viruses of food origin. Results showed that 25% (19/76) of the samples contained at least one another mammal-associated virus, notably alphacoronaviruses (13/76) such as AlphaCoV/YN2012, HKU2-related CoV and AlphaCoV/Rf-HuB2013, along with viruses from other families. Notably, we observed three viruses co-circulating within a single bat, comprising two coronavirus species and one picornavirus. Our analysis also revealed the potential presence of pathogenic bacteria or fungi in bats. Furthermore, we obtained 25 viral genomes from the 76 bat SARSr-CoV positive samples, some of which formed new evolutionary lineages. Collectively, our study reveals the complex microenvironment of bat microbiome, facilitating deeper investigations into their pathogenic potential and the likelihood of cross-species transmission.
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Affiliation(s)
- Hao-Rui Si
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 43000, China; University of Chinese Academy of Sciences, Beijing 100000, China
| | - Ke Wu
- Guangzhou National Laboratory, Guangzhou International Bio Island, Guangzhou 510005, China
| | - Jia Su
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 43000, China; University of Chinese Academy of Sciences, Beijing 100000, China
| | - Tian-Yi Dong
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 43000, China; University of Chinese Academy of Sciences, Beijing 100000, China
| | - Yan Zhu
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 43000, China
| | - Bei Li
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 43000, China
| | - Ying Chen
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 43000, China
| | - Yang Li
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 43000, China
| | - Zheng-Li Shi
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 43000, China; Guangzhou National Laboratory, Guangzhou International Bio Island, Guangzhou 510005, China.
| | - Peng Zhou
- Guangzhou National Laboratory, Guangzhou International Bio Island, Guangzhou 510005, China; State Key Laboratory of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical School, Guangzhou 510005, China.
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2
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Prentice MB, Gilbertson MLJ, Storm DJ, Turner WC, Walsh DP, Pinkerton ME, Kamath PL. Metagenomic sequencing sheds light on microbes putatively associated with pneumonia-related fatalities of white-tailed deer ( Odocoileus virginianus). Microb Genom 2024; 10:001214. [PMID: 38536208 PMCID: PMC10995629 DOI: 10.1099/mgen.0.001214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 02/27/2024] [Indexed: 04/07/2024] Open
Abstract
With emerging infectious disease outbreaks in human, domestic and wild animal populations on the rise, improvements in pathogen characterization and surveillance are paramount for the protection of human and animal health, as well as the conservation of ecologically and economically important wildlife. Genomics offers a range of suitable tools to meet these goals, with metagenomic sequencing facilitating the characterization of whole microbial communities associated with emerging and endemic disease outbreaks. Here, we use metagenomic sequencing in a case-control study to identify microbes in lung tissue associated with newly observed pneumonia-related fatalities in 34 white-tailed deer (Odocoileus virginianus) in Wisconsin, USA. We identified 20 bacterial species that occurred in more than a single individual. Of these, only Clostridium novyi was found to substantially differ (in number of detections) between case and control sample groups; however, this difference was not statistically significant. We also detected several bacterial species associated with pneumonia and/or other diseases in ruminants (Mycoplasma ovipneumoniae, Trueperella pyogenes, Pasteurella multocida, Anaplasma phagocytophilum, Fusobacterium necrophorum); however, these species did not substantially differ between case and control sample groups. On average, we detected a larger number of bacterial species in case samples than controls, supporting the potential role of polymicrobial infections in this system. Importantly, we did not detect DNA of viruses or fungi, suggesting that they are not significantly associated with pneumonia in this system. Together, these results highlight the utility of metagenomic sequencing for identifying disease-associated microbes. This preliminary list of microbes will help inform future research on pneumonia-associated fatalities of white-tailed deer.
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Affiliation(s)
| | - Marie L. J. Gilbertson
- Wisconsin Cooperative Wildlife Research Unit, Department of Forest and Wildlife Ecology, University of Wisconsin-Madison, Wisconsin, USA
| | | | - Wendy C. Turner
- U.S. Geological Survey, Wisconsin Cooperative Wildlife Research Unit, Department of Forest and Wildlife Ecology, University of Wisconsin-Madison, Wisconsin, USA
| | - Daniel P. Walsh
- U.S. Geological Survey, Montana Cooperative Wildlife Research Unit, University of Montana, Montana, USA
| | - Marie E. Pinkerton
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Wisconsin, USA
| | - Pauline L. Kamath
- School of Food and Agriculture, University of Maine, Maine, USA
- Maine Center for Genetics in the Environment, University of Maine, Orono, Maine, USA
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3
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Couto RDS, Ramos EDSF, Abreu WU, Rodrigues LRR, Marinho LF, Morais VDS, Villanova F, Pandey RP, Deng X, Delwart E, da Costa AC, Leal E. Metagenomic of Liver Tissue Identified at Least Two Genera of Totivirus-like Viruses in Molossus molossus Bats. Microorganisms 2024; 12:206. [PMID: 38276191 PMCID: PMC10819564 DOI: 10.3390/microorganisms12010206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 01/15/2024] [Accepted: 01/16/2024] [Indexed: 01/27/2024] Open
Abstract
The Totiviridae family of viruses has a unique genome consisting of double-stranded RNA with two open reading frames that encode the capsid protein (Cap) and the RNA-dependent RNA polymerase (RdRpol). Most virions in this family are isometric in shape, approximately 40 nm in diameter, and lack an envelope. There are five genera within this family, including Totivirus, Victorivirus, Giardiavirus, Leishmaniavirus, and Trichomonasvirus. While Totivirus and Victorivirus primarily infect fungi, Giardiavirus, Leishmaniavirus, and Trichomonasvirus infect diverse hosts, including protists, insects, and vertebrates. Recently, new totivirus-like species have been discovered in fish and plant hosts, and through metagenomic analysis, a novel totivirus-like virus (named Tianjin totivirus) has been isolated from bat guano. Interestingly, Tianjin totivirus causes cytopathic effects in insect cells but cannot grow in mammalian cells, suggesting that it infects insects consumed by insectivorous bats. In this study, we used next-generation sequencing and identified totivirus-like viruses in liver tissue from Molossus molossus bats in the Amazon region of Brazil. Comparative phylogenetic analysis based on the RNA-dependent RNA polymerase region revealed that the viruses identified in Molossus bats belong to two distinct phylogenetic clades, possibly comprising different genera within the Totiviridae family. Notably, the mean similarity between the Tianjin totivirus and the totiviruses identified in Molossus bats is less than 18%. These findings suggest that the diversity of totiviruses in bats is more extensive than previously recognized and highlight the potential for bats to serve as reservoirs for novel toti-like viruses.
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Affiliation(s)
- Roseane da Silva Couto
- Laboratório de Diversidade Viral, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belem 66075-000, PA, Brazil; (R.d.S.C.); (E.d.S.F.R.); (F.V.)
| | - Endrya do Socorro Foro Ramos
- Laboratório de Diversidade Viral, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belem 66075-000, PA, Brazil; (R.d.S.C.); (E.d.S.F.R.); (F.V.)
| | - Wandercleyson Uchôa Abreu
- Programa de Pos-Graduação REDE Bionorte, Polo Pará, Universidade Federal do Oeste do Pará, Santarém 68040-255, PA, Brazil;
| | - Luis Reginaldo Ribeiro Rodrigues
- Laboratory of Genetics & Biodiversity, Institute of Educational Sciences, Universidade Federal do Oeste do Pará, Santarém 68040-255, PA, Brazil;
| | | | - Vanessa dos Santos Morais
- Laboratory of Virology (LIM 52), Instituto de Medicina Tropical, Universidade de São Paulo, São Paulo 05403-000, SP, Brazil; (V.d.S.M.); (A.C.d.C.)
| | - Fabiola Villanova
- Laboratório de Diversidade Viral, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belem 66075-000, PA, Brazil; (R.d.S.C.); (E.d.S.F.R.); (F.V.)
| | - Ramendra Pati Pandey
- School of Health Sciences and Technology (SoHST), UPES, Dehradun 248007, Uttarakhand, India;
| | - Xutao Deng
- Vitalant Research Institute, San Francisco, CA 94143, USA;
| | - Eric Delwart
- Department Laboratory Medicine, University of California San Francisco, San Francisco, CA 94143, USA;
| | - Antonio Charlys da Costa
- Laboratory of Virology (LIM 52), Instituto de Medicina Tropical, Universidade de São Paulo, São Paulo 05403-000, SP, Brazil; (V.d.S.M.); (A.C.d.C.)
| | - Elcio Leal
- Laboratório de Diversidade Viral, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belem 66075-000, PA, Brazil; (R.d.S.C.); (E.d.S.F.R.); (F.V.)
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Chan TTY, Chow FWN, Fung J, Cheng FKK, Lo GCS, Tsang CC, Luk HKH, Wong ACP, He Z, Aw-Yong KL, Liu X, Yuen KY, Woo PCY, Lau SKP. A sensitive and simple RT-LAMP assay for sarbecovirus screening in bats. Microbiol Spectr 2023; 11:e0259123. [PMID: 37971222 PMCID: PMC10715088 DOI: 10.1128/spectrum.02591-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 10/10/2023] [Indexed: 11/19/2023] Open
Abstract
IMPORTANCE We report the application of a colorimetric and fluorescent reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay to facilitate mass screening for sarbecoviruses in bats. The assay was evaluated using a total of 838 oral and alimentary samples from bats and demonstrated comparable sensitivity and specificity to quantitative reverse transcription PCR (qRT-PCR), with a simple setup. The addition of SYTO9, a fluorescent nucleic acid stain, also allows for quantitative analysis. The scalability and simplicity of the assay are believed to contribute to improving preparedness for detecting emerging coronaviruses by applying it to field studies and surveillance.
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Affiliation(s)
- Tony Tat-Yin Chan
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Franklin Wang-Ngai Chow
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong, China
| | - Joshua Fung
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong, China
| | - Flora Ka-Kei Cheng
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - George Chi-Shing Lo
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Chi-Ching Tsang
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
- School of Medical and Health Sciences, Tung Wah College, Hong Kong, China
| | - Hayes Kam-Hei Luk
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Antonio Cheuk-Pui Wong
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Zirong He
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Kam Leng Aw-Yong
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Xueyan Liu
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Kwok-Yung Yuen
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Patrick Chiu-Yat Woo
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
- Doctoral Program in Translational Medicine and Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan
- The iEGG and Animal Biotechnology Research Center, National Chung Hsing University, Taichung, Taiwan
| | - Susanna Kar-Pui Lau
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
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5
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Jones BD, Kaufman EJ, Peel AJ. Viral Co-Infection in Bats: A Systematic Review. Viruses 2023; 15:1860. [PMID: 37766267 PMCID: PMC10535902 DOI: 10.3390/v15091860] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 08/28/2023] [Accepted: 08/29/2023] [Indexed: 09/29/2023] Open
Abstract
Co-infection is an underappreciated phenomenon in contemporary disease ecology despite its ubiquity and importance in nature. Viruses, and other co-infecting agents, can interact in ways that shape host and agent communities, influence infection dynamics, and drive evolutionary selective pressures. Bats are host to many viruses of zoonotic potential and have drawn increasing attention in their role as wildlife reservoirs for human spillover. However, the role of co-infection in driving viral transmission dynamics within bats is unknown. Here, we systematically review peer-reviewed literature reporting viral co-infections in bats. We show that viral co-infection is common in bats but is often only reported as an incidental finding. Biases identified in our study database related to virus and host species were pre-existing in virus studies of bats generally. Studies largely speculated on the role co-infection plays in viral recombination and few investigated potential drivers or impacts of co-infection. Our results demonstrate that current knowledge of co-infection in bats is an ad hoc by-product of viral discovery efforts, and that future targeted co-infection studies will improve our understanding of the role it plays. Adding to the broader context of co-infection studies in other wildlife species, we anticipate our review will inform future co-infection study design and reporting in bats. Consideration of detection strategy, including potential viral targets, and appropriate analysis methodology will provide more robust results and facilitate further investigation of the role of viral co-infection in bat reservoirs.
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Affiliation(s)
- Brent D. Jones
- Centre for Planetary Health and Food Security, Griffith University, Nathan, QLD 4111, Australia
- School of Environment and Science, Griffith University, Nathan, QLD 4111, Australia
| | | | - Alison J. Peel
- Centre for Planetary Health and Food Security, Griffith University, Nathan, QLD 4111, Australia
- School of Environment and Science, Griffith University, Nathan, QLD 4111, Australia
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6
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Nibert ML, Xie Y, Xiao J, Gao Y, Liu D, Yang G, Tao J. Transcriptome mining of RNA viruses (family Totiviridae ) in Eimeria necatrix and Eimeria stiedai. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.20.541574. [PMID: 37292684 PMCID: PMC10245732 DOI: 10.1101/2023.05.20.541574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Coccidian protozoa from the genus Eimeria are widespread parasites of vertebrates, causing serious disease (coccidiosis) and economic loss most notably in poultry. Several species of Eimeria are themselves infected with small RNA viruses assigned to the family Totiviridae . In this study, the sequences of two such viruses were newly determined, one of which represents the first complete protein-coding sequence of a virus from E. necatrix , an important pathogen of chickens, and the other of which is from E. stiedai , an important pathogen of rabbits. Sequence features of the newly identified viruses, compared with those of ones reported previously, provide several insights. Phylogenetic analyses suggest that these eimerian viruses constitute a well-demarcated clade, probably deserving of recognition as a distinct genus.
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7
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Ortiz-Baez AS, Jaenson TGT, Holmes EC, Pettersson JHO, Wilhelmsson P. Substantial viral and bacterial diversity at the bat-tick interface. Microb Genom 2023; 9. [PMID: 36862584 PMCID: PMC10132063 DOI: 10.1099/mgen.0.000942] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2023] Open
Abstract
Ticks harbour a high diversity of viruses, bacteria and protozoa. The soft tick Carios vespertilionis (Argasidae) is a common ectoparasite of bats in the Palearctic region and is suspected to be vector and reservoir of viruses and other microbial species in bat populations, some of which may act as zoonotic agents for human disease. The Soprano pipistrelle (Pipistrellus pygmaeus, Vespertilionidae) is widely distributed in Europe, where it can be found inside or close to human habitation. We used meta-transcriptomic sequencing to determine the RNA virome and common microbiota in blood-fed C. vespertilionis ticks collected from a Soprano pipistrelle bat roosting site in south-central Sweden. Our analyses identified 16 viruses from 11 virus families, of which 15 viruses were novel. For the first time in Sweden we identified Issuk-Kul virus, a zoonotic arthropod-borne virus previously associated with outbreaks of acute febrile illness in humans. Probable bat-associated and tick-borne viruses were classified within the families Nairoviridae, Caliciviridae and Hepeviridae, while other invertebrate-associated viruses included members of the Dicistroviridae, Iflaviridae, Nodaviridae, Partitiviridae, Permutotetraviridae, Polycipiviridae and Solemoviridae. Similarly, we found abundant bacteria in C. vespertilionis, including genera with known tick-borne bacteria, such as Coxiella spp. and Rickettsia spp. These findings demonstrate the remarkable diversity of RNA viruses and bacteria present in C. vespertilionis and highlight the importance of bat-associated ectoparasite surveillance as an effective and non-invasive means to track viruses and bacteria circulating in bats and ticks.
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Affiliation(s)
- Ayda Susana Ortiz-Baez
- Sydney Institute for Infectious Diseases, School of Medical Sciences, the University of Sydney, Sydney, New South Wales 2006, Australia
| | - Thomas G T Jaenson
- Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, SE-752 36, Uppsala, Sweden
| | - Edward C Holmes
- Sydney Institute for Infectious Diseases, School of Medical Sciences, the University of Sydney, Sydney, New South Wales 2006, Australia
| | - John H-O Pettersson
- Sydney Institute for Infectious Diseases, School of Medical Sciences, the University of Sydney, Sydney, New South Wales 2006, Australia.,Zoonosis Science Center, Department of Medical Biochemistry and Microbiology, University of Uppsala, SE-751 23 Uppsala, Sweden.,Clinical Microbiology and Hospital Hygiene, Uppsala University Hospital, 75237 Uppsala, Sweden
| | - Peter Wilhelmsson
- Department of Biomedical and Clinical Sciences, Division of Inflammation and Infection, Linköping University, SE-581 83 Linköping, Sweden.,Department of Clinical Microbiology, Region Jönköping County, SE-553 05 Jönköping, Sweden
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8
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Detection of coronaviruses in insectivorous bats of Fore-Caucasus, 2021. Sci Rep 2023; 13:2306. [PMID: 36759670 PMCID: PMC9909659 DOI: 10.1038/s41598-023-29099-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 01/30/2023] [Indexed: 02/11/2023] Open
Abstract
Coronaviruses (CoVs) pose a huge threat to public health as emerging viruses. Bat-borne CoVs are especially unpredictable in their evolution due to some unique features of bat physiology boosting the rate of mutations in CoVs, which is already high by itself compared to other viruses. Among bats, a meta-analysis of overall CoVs epizootiology identified a nucleic acid observed prevalence of 9.8% (95% CI 8.7-10.9%). The main objectives of our study were to conduct a qPCR screening of CoVs' prevalence in the insectivorous bat population of Fore-Caucasus and perform their characterization based on the metagenomic NGS of samples with detected CoV RNA. According to the qPCR screening, CoV RNA was detected in 5 samples, resulting in a 3.33% (95% CI 1.1-7.6%) prevalence of CoVs in bats from these studied locations. BetaCoVs reads were identified in raw metagenomic NGS data, however, detailed characterization was not possible due to relatively low RNA concentration in samples. Our results correspond to other studies, although a lower prevalence in qPCR studies was observed compared to other regions and countries. Further studies should require deeper metagenomic NGS investigation, as a supplementary method, which will allow detailed CoV characterization.
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9
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Cholleti H, de Jong J, Blomström AL, Berg M. Investigation of the Virome and Characterization of Issyk-Kul Virus from Swedish Myotis brandtii Bats. Pathogens 2022; 12:pathogens12010012. [PMID: 36678360 PMCID: PMC9861107 DOI: 10.3390/pathogens12010012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 12/19/2022] [Accepted: 12/20/2022] [Indexed: 12/24/2022] Open
Abstract
Bats are reservoirs for many different viruses, including some that can be transmitted to and cause disease in humans and/or animals. However, less is known about the bat-borne viruses circulating in Northern European countries such as in Sweden. In this study, saliva from Myotis brandtii bats, collected from south-central Sweden, was analyzed for viruses. The metagenomic analysis identified viral sequences belonging to different viral families, including, e.g., Nairoviridae, Retroviridae, Poxviridae, Herpesviridae and Siphoviridae. Interestingly, through the data analysis, the near-complete genome of Issyk-Kul virus (ISKV), a zoonotic virus within the Nairoviridae family, was obtained, showing 95-99% protein sequence identity to previously described ISKVs. This virus is believed to infect humans via an intermediate tick host or through contact with bat excrete. ISKV has previously been found in bats in Europe, but not previously in the Nordic region. In addition, near full-length genomes of two novel viruses belonging to Picornavirales order and Tymoviridae family were characterized. Taken together, our study has not only identified novel viruses, but also the presence of a zoonotic virus not previously known to circulate in this region. Thus, the results from these types of studies can help us to better understand the diversity of viruses circulating in bat populations, as well as identify viruses with zoonotic potential that could possibly be transmitted to humans.
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Affiliation(s)
- Harindranath Cholleti
- Section of Virology, Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences (SLU), P.O. Box 7028, 750 07 Uppsala, Sweden
- Correspondence:
| | - Johnny de Jong
- Swedish Biodiversity Centre (CBM), SLU, P.O. Box 7016, 750 07 Uppsala, Sweden
| | - Anne-Lie Blomström
- Section of Virology, Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences (SLU), P.O. Box 7028, 750 07 Uppsala, Sweden
| | - Mikael Berg
- Section of Virology, Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences (SLU), P.O. Box 7028, 750 07 Uppsala, Sweden
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10
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Kamau J, Ergunay K, Webala PW, Justi SA, Bourke BP, Kamau MW, Hassell J, Chege MN, Mwaura DK, Simiyu C, Kibiwot S, Onyuok S, Caicedo-Quiroga L, Li T, Zimmerman DM, Linton YM. A Novel Coronavirus and a Broad Range of Viruses in Kenyan Cave Bats. Viruses 2022; 14:v14122820. [PMID: 36560824 PMCID: PMC9785147 DOI: 10.3390/v14122820] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 12/12/2022] [Accepted: 12/15/2022] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND AND METHODS To investigate virus diversity in hot zones of probable pathogen spillover, 54 oral-fecal swabs were processed from five bat species collected from three cave systems in Kenya, using metagenome sequencing. RESULTS Viruses belonging to the Astroviridae, Circoviridae, Coronaviridae, Dicistroviridae, Herpesviridae and Retroviridae were detected, with unclassified viruses. Retroviral sequences were prevalent; 74.1% of all samples were positive, with distinct correlations between virus, site and host bat species. Detected retroviruses comprised Myotis myotis, Myotis ricketti, Myotis daubentonii and Galidia endogenous retroviruses, murine leukemia virus-related virus and Rhinolophus ferrumequinum retrovirus (RFRV). A near-complete genome of a local RFRV strain with identical genome organization and 2.8% nucleotide divergence from the prototype isolate was characterized. Bat coronavirus sequences were detected with a prevalence of 24.1%, where analyses on the ORF1ab region revealed a novel alphacoronavirus lineage. Astrovirus sequences were detected in 25.9%of all samples, with considerable diversity. In 9.2% of the samples, other viruses including Actinidia yellowing virus 2, bat betaherpesvirus, Bole tick virus 4, Cyclovirus and Rhopalosiphum padi virus were identified. CONCLUSIONS Further monitoring of bats across Kenya is essential to facilitate early recognition of possibly emergent zoonotic viruses.
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Affiliation(s)
- Joseph Kamau
- One Health Centre, Institute of Primate Research (IPR), Nairobi 00502, Kenya
| | - Koray Ergunay
- Walter Reed Biosystematics Unit (WRBU), Smithsonian Institution Museum Support Center, Suitland, MD 20746, USA
- One Health Branch, Walter Reed Army Institute of Research (WRAIR), Silver Spring, MD 20910, USA
- Department of Medical Microbiology, Virology Unit, Faculty of Medicine, Hacettepe University, Ankara 06230, Turkey
- Department of Entomology, Smithsonian Institution–National Museum of Natural History (NMNH), Washington, DC 20560, USA
- Correspondence:
| | - Paul W. Webala
- Department of Forestry and Wildlife Management, Maasai Mara University, Narok 20500, Kenya
| | - Silvia A. Justi
- Walter Reed Biosystematics Unit (WRBU), Smithsonian Institution Museum Support Center, Suitland, MD 20746, USA
- One Health Branch, Walter Reed Army Institute of Research (WRAIR), Silver Spring, MD 20910, USA
- Department of Entomology, Smithsonian Institution–National Museum of Natural History (NMNH), Washington, DC 20560, USA
| | - Brian P. Bourke
- Walter Reed Biosystematics Unit (WRBU), Smithsonian Institution Museum Support Center, Suitland, MD 20746, USA
- One Health Branch, Walter Reed Army Institute of Research (WRAIR), Silver Spring, MD 20910, USA
- Department of Entomology, Smithsonian Institution–National Museum of Natural History (NMNH), Washington, DC 20560, USA
| | - Maureen W. Kamau
- Mpala Research Centre, Nanyuki 10400, Kenya
- Global Health Program, Smithsonian Conservation Biology Institute (SCBI), Front Royal, VA 22630, USA
| | - James Hassell
- Mpala Research Centre, Nanyuki 10400, Kenya
- Department of Epidemiology of Microbial Disease, Yale School of Public Health, New Haven, CT 06520, USA
- International Livestock Research Institute (ILRI), Nairobi 00100, Kenya
| | - Mary N. Chege
- One Health Centre, Institute of Primate Research (IPR), Nairobi 00502, Kenya
| | - David K. Mwaura
- One Health Centre, Institute of Primate Research (IPR), Nairobi 00502, Kenya
| | - Cynthia Simiyu
- Department of Forestry and Wildlife Management, Maasai Mara University, Narok 20500, Kenya
| | - Sospeter Kibiwot
- Department of Forestry and Wildlife Management, Maasai Mara University, Narok 20500, Kenya
| | - Samson Onyuok
- Zoology Department, National Museums of Kenya, Nairobi 00100, Kenya
| | - Laura Caicedo-Quiroga
- Walter Reed Biosystematics Unit (WRBU), Smithsonian Institution Museum Support Center, Suitland, MD 20746, USA
- One Health Branch, Walter Reed Army Institute of Research (WRAIR), Silver Spring, MD 20910, USA
- Department of Entomology, Smithsonian Institution–National Museum of Natural History (NMNH), Washington, DC 20560, USA
| | - Tao Li
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - Dawn M. Zimmerman
- Walter Reed Biosystematics Unit (WRBU), Smithsonian Institution Museum Support Center, Suitland, MD 20746, USA
- Department of Entomology, Smithsonian Institution–National Museum of Natural History (NMNH), Washington, DC 20560, USA
- Zoology Department, National Museums of Kenya, Nairobi 00100, Kenya
| | - Yvonne-Marie Linton
- Walter Reed Biosystematics Unit (WRBU), Smithsonian Institution Museum Support Center, Suitland, MD 20746, USA
- One Health Branch, Walter Reed Army Institute of Research (WRAIR), Silver Spring, MD 20910, USA
- Department of Entomology, Smithsonian Institution–National Museum of Natural History (NMNH), Washington, DC 20560, USA
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11
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Schmid DW, Fackelmann G, Wasimuddin, Rakotondranary J, Ratovonamana YR, Montero BK, Ganzhorn JU, Sommer S. A framework for testing the impact of co-infections on host gut microbiomes. Anim Microbiome 2022; 4:48. [PMID: 35945629 PMCID: PMC9361228 DOI: 10.1186/s42523-022-00198-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 07/26/2022] [Indexed: 02/07/2023] Open
Abstract
Parasitic infections disturb gut microbial communities beyond their natural range of variation, possibly leading to dysbiosis. Yet it remains underappreciated that most infections are accompanied by one or more co-infections and their collective impact is largely unexplored. Here we developed a framework illustrating changes to the host gut microbiome following single infections, and build on it by describing the neutral, synergistic or antagonistic impacts on microbial α- and ß-diversity expected from co-infections. We tested the framework on microbiome data from a non-human primate population co-infected with helminths and Adenovirus, and matched patterns reported in published studies to the introduced framework. In this case study, α-diversity of co-infected Malagasy mouse lemurs (Microcebus griseorufus) did not differ in comparison with that of singly infected or uninfected individuals, even though community composition captured with ß-diversity metrices changed significantly. Explicitly, we record stochastic changes in dispersion, a sign of dysbiosis, following the Anna-Karenina principle rather than deterministic shifts in the microbial gut community. From the literature review and our case study, neutral and synergistic impacts emerged as common outcomes from co-infections, wherein both shifts and dispersion of microbial communities following co-infections were often more severe than after a single infection alone, but microbial α-diversity was not universally altered. Important functions of the microbiome may also suffer from such heavily altered, though no less species-rich microbial community. Lastly, we pose the hypothesis that the reshuffling of host-associated microbial communities due to the impact of various, often coinciding parasitic infections may become a source of novel or zoonotic diseases.
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12
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Cholleti H, de Jong J, Blomström AL, Berg M. Characterization of Pipistrellus pygmaeus Bat Virome from Sweden. Viruses 2022; 14:v14081654. [PMID: 36016275 PMCID: PMC9415950 DOI: 10.3390/v14081654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 06/27/2022] [Accepted: 07/24/2022] [Indexed: 11/25/2022] Open
Abstract
Increasing amounts of data indicate that bats harbor a higher viral diversity relative to other mammalian orders, and they have been recognized as potential reservoirs for pathogenic viruses, such as the Hendra, Nipah, Marburg, and SARS-CoV viruses. Here, we present the first viral metagenomic analysis of Pipistrellus pygmaeus from Uppsala, Sweden. Total RNA was extracted from the saliva and feces of individual bats and analyzed using Illumina sequencing. The results identified sequences related to 51 different viral families, including vertebrate, invertebrate, and plant viruses. These viral families include Coronaviridae, Picornaviridae, Dicistroviridae, Astroviridae, Hepeviridae, Reoviridae, Botourmiaviridae, Lispviridae, Totiviridae, Botoumiaviridae, Parvoviridae, Retroviridae, Adenoviridae, and Partitiviridae, as well as different unclassified viruses. We further characterized three near full-length genome sequences of bat coronaviruses. A phylogenetic analysis showed that these belonged to alphacoronaviruses with the closest similarity (78–99% at the protein level) to Danish and Finnish bat coronaviruses detected in Pipistrellus and Myotis bats. In addition, the full-length and the near full-length genomes of picornavirus were characterized. These showed the closest similarity (88–94% at the protein level) to bat picornaviruses identified in Chinese bats. Altogether, the results of this study show that Swedish Pipistrellus bats harbor a great diversity of viruses, some of which are closely related to mammalian viruses. This study expands our knowledge on the bat population virome and improves our understanding of the evolution and transmission of viruses among bats and to other species.
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Affiliation(s)
- Harindranath Cholleti
- Section of Virology, Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences (SLU), P.O. Box 7028, 750 07 Uppsala, Sweden; (A.-L.B.); (M.B.)
- Correspondence:
| | - Johnny de Jong
- Swedish Biodiversity Centre (CBM), Department of Urban and Rural Development, Swedish University of Agricultural Sciences (SLU), P.O. Box 7016, 750 07 Uppsala, Sweden;
| | - Anne-Lie Blomström
- Section of Virology, Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences (SLU), P.O. Box 7028, 750 07 Uppsala, Sweden; (A.-L.B.); (M.B.)
| | - Mikael Berg
- Section of Virology, Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences (SLU), P.O. Box 7028, 750 07 Uppsala, Sweden; (A.-L.B.); (M.B.)
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13
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Vanmechelen B, Meurs S, Horemans M, Loosen A, Joly Maes T, Laenen L, Vergote V, Koundouno FR, Magassouba N, Konde MK, Condé IS, Carroll MW, Maes P. The Characterization of Multiple Novel Paramyxoviruses Highlights the Diverse Nature of the Subfamily Orthoparamyxovirinae. Virus Evol 2022; 8:veac061. [PMID: 35854826 PMCID: PMC9290864 DOI: 10.1093/ve/veac061] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 05/14/2022] [Accepted: 06/29/2022] [Indexed: 11/26/2022] Open
Abstract
The subfamily Orthoparamyxovirinae is a group of single-stranded, negative-sense RNA viruses that contains many human, animal, and zoonotic pathogens. While there are currently only forty-two recognized species in this subfamily, recent research has revealed that much of its diversity remains to be characterized. Using a newly developed nested PCR-based screening assay, we report here the discovery of fifteen orthoparamyxoviruses in rodents and shrews from Belgium and Guinea, thirteen of which are believed to represent new species. Using a combination of nanopore and sanger sequencing, complete genomes could be determined for almost all these viruses, enabling a detailed evaluation of their genome characteristics. While most viruses are thought to belong to the rapidly expanding genus Jeilongvirus, we also identify novel members of the genera Narmovirus, Henipavirus, and Morbillivirus. Together with other recently discovered orthoparamyxoviruses, both henipaviruses and the morbillivirus discovered here appear to form distinct rodent-/shrew-borne clades within their respective genera, clustering separately from all currently classified viruses. In the case of the henipaviruses, a comparison of the different members of this clade revealed the presence of a secondary conserved open reading frame, encoding for a transmembrane protein, within the F gene, the biological relevance of which remains to be established. While the characteristics of the viruses described here shed further light on the complex evolutionary origin of paramyxoviruses, they also illustrate that the diversity of this group of viruses in terms of genome organization appears to be much larger than previously assumed.
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Affiliation(s)
- Bert Vanmechelen
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Laboratory of Clinical and Epidemiological Virology, Rega Institute for Medical Research , Herestraat 49/Box 1040, BE3000 Leuven, Belgium
| | - Sien Meurs
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Laboratory of Clinical and Epidemiological Virology, Rega Institute for Medical Research , Herestraat 49/Box 1040, BE3000 Leuven, Belgium
| | - Marie Horemans
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Laboratory of Clinical and Epidemiological Virology, Rega Institute for Medical Research , Herestraat 49/Box 1040, BE3000 Leuven, Belgium
| | - Arne Loosen
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Laboratory of Clinical and Epidemiological Virology, Rega Institute for Medical Research , Herestraat 49/Box 1040, BE3000 Leuven, Belgium
| | - Tibe Joly Maes
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Laboratory of Clinical and Epidemiological Virology, Rega Institute for Medical Research , Herestraat 49/Box 1040, BE3000 Leuven, Belgium
| | - Lies Laenen
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Laboratory of Clinical and Epidemiological Virology, Rega Institute for Medical Research , Herestraat 49/Box 1040, BE3000 Leuven, Belgium
| | - Valentijn Vergote
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Laboratory of Clinical and Epidemiological Virology, Rega Institute for Medical Research , Herestraat 49/Box 1040, BE3000 Leuven, Belgium
| | - Fara Raymond Koundouno
- Laboratoire des fièvres hémorragiques et virales de Guinée , Conakry Guinea – Direction préfectorale de la santé de Gueckedou
| | - N’Faly Magassouba
- Projet des Fièvres Hémorragiques en Guinée, Laboratoire de Recherche en Virologie , Conakry, Guinea
| | - Mandy Kader Konde
- Center of Excellence for Training, Research on Malaria and Disease Control in Guinea (CEFORPAG) , Quartier Nongo, Ratoma, Conakry, Guinea
| | - Ibrahima Sory Condé
- Center of Excellence for Training, Research on Malaria and Disease Control in Guinea (CEFORPAG) , Quartier Nongo, Ratoma, Conakry, Guinea
| | - Miles W Carroll
- Pandemic Science Centre, Oxford University, Nuffield Department of Medicine, Wellcome Centre for Human Genetics , CCMP1st South, Roosevelt Dr, Headington, Oxford OX3 7BN, United Kingdom
| | - Piet Maes
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Laboratory of Clinical and Epidemiological Virology, Rega Institute for Medical Research , Herestraat 49/Box 1040, BE3000 Leuven, Belgium
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14
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Abstract
The coronavirus disease 2019 (COVID-19) pandemic has had a profound impact on human health, economic well-being, and societal function. It is essential that we use this generational experience to better understand the processes that underpin the emergence of COVID-19 and other zoonotic diseases. Herein, I review the mechanisms that determine why and how viruses emerge in new hosts, as well as the barriers to this process. I show that traditional studies of virus emergence have an inherent anthropocentric bias, with disease in humans considered the inevitable outcome of virus emergence, when in reality viruses are integral components of a global ecosystem characterized by continual host jumping with humans also transmitting their viruses to other animals. I illustrate these points using coronaviruses, including severe acute respiratory syndrome coronavirus 2, as a case study. I also outline the potential steps that can be followed to help mitigate and prevent future pandemics, with combating climate change a central component. Expected final online publication date for the Annual Review of Virology, Volume 9 is September 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Edward C Holmes
- Sydney Institute for Infectious Diseases, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, New South Wales, Australia;
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15
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Abstract
The COVID-19 pandemic has given the study of virus evolution and ecology new relevance. Although viruses were first identified more than a century ago, we likely know less about their diversity than that of any other biological entity. Most documented animal viruses have been sampled from just two phyla - the Chordata and the Arthropoda - with a strong bias towards viruses that infect humans or animals of economic and social importance, often in association with strong disease phenotypes. Fortunately, the recent development of unbiased metagenomic next-generation sequencing is providing a richer view of the animal virome and shedding new light on virus evolution. In this Review, we explore our changing understanding of the diversity, composition and evolution of the animal virome. We outline the factors that determine the phylogenetic diversity and genomic structure of animal viruses on evolutionary timescales and show how this impacts assessment of the risk of disease emergence in the short term. We also describe the ongoing challenges in metagenomic analysis and outline key themes for future research. A central question is how major events in the evolutionary history of animals, such as the origin of the vertebrates and periodic mass extinction events, have shaped the diversity and evolution of the viruses they carry.
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16
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Zoonotic disease and virome diversity in bats. Curr Opin Virol 2021; 52:192-202. [PMID: 34954661 PMCID: PMC8696223 DOI: 10.1016/j.coviro.2021.12.008] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 11/19/2021] [Accepted: 12/06/2021] [Indexed: 02/08/2023]
Abstract
The emergence of zoonotic viral diseases in humans commonly reflects exposure to mammalian wildlife. Bats (order Chiroptera) are arguably the most important mammalian reservoir for zoonotic viruses, with notable examples including Severe Acute Respiratory Syndrome coronaviruses 1 and 2, Middle East Respiratory Syndrome coronavirus, henipaviruses and lyssaviruses. Herein, we outline our current knowledge on the diversity of bat viromes, particularly through the lens of metagenomic next-generation sequencing and in the context of disease emergence. A key conclusion is that although bats harbour abundant virus diversity, the vast majority of bat viruses have not emerged to cause disease in new hosts such that bats are better regarded as critical but endangered components of global ecosystems.
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17
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Abstract
Bats are infamous reservoirs of deadly human viruses. While retroviruses, such as the human immunodeficiency virus (HIV), are among the most significant of virus families that have jumped from animals into humans, whether bat retroviruses have the potential to infect and cause disease in humans remains unknown. Recent reports of retroviruses circulating in bat populations builds on two decades of research describing the fossil records of retroviral sequences in bat genomes and of viral metagenomes extracted from bat samples. The impact of the global COVID-19 pandemic demands that we pay closer attention to viruses hosted by bats and their potential as a zoonotic threat. Here we review current knowledge of bat retroviruses and explore the question of whether they represent a threat to humans.
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Affiliation(s)
- Joshua A. Hayward
- Health Security Program, Life Sciences Discipline, Burnet Institute, Melbourne, VIC, Australia
- Department of Microbiology, Monash University, Clayton, VIC, Australia
| | - Gilda Tachedjian
- Health Security Program, Life Sciences Discipline, Burnet Institute, Melbourne, VIC, Australia
- Department of Microbiology, Monash University, Clayton, VIC, Australia
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC, Australia
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18
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Update on Potentially Zoonotic Viruses of European Bats. Vaccines (Basel) 2021; 9:vaccines9070690. [PMID: 34201666 PMCID: PMC8310327 DOI: 10.3390/vaccines9070690] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 06/10/2021] [Accepted: 06/21/2021] [Indexed: 12/13/2022] Open
Abstract
Bats have been increasingly gaining attention as potential reservoir hosts of some of the most virulent viruses known. Numerous review articles summarize bats as potential reservoir hosts of human-pathogenic zoonotic viruses. For European bats, just one review article is available that we published in 2014. The present review provides an update on the earlier article and summarizes the most important viruses found in European bats and their possible implications for Public Health. We identify the research gaps and recommend monitoring of these viruses.
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